Delphy

Delphy

[](https://github.com/broadinstitute/delphy/actions/workflows/ci.yml) [](https://codecov.io/gh/broadinstitute/delphy) [](https://github.com/broadinstitute/delphy/pkgs/container/delphy) [](https://doi.org/10.5281/zenodo.11922813)

Delphy is a fast, scalable, accurate and accessible tool for Bayesian phylogenetics based on Explicit Mutation-Annotated Trees (EMATs). EMATs are an extension of the Mutation-Annotated Trees (MATs) introduced by [UShER](https://github.com/yatisht/usher) where nodes have explicit times, mutations are represented as explicit timed events along branches, and missing data is explicitly represented. EMATs open substantial simplifications and scaling opportunities in the calculations powering Bayesian phylogenetics, at the cost of some statistical efficiency with respect to the traditional calculations based on Felsenstein pruning. For genomic epidemiology datasets, where the total number of mutations on a tree is comparable to the number of samples, this is a very favorable trade-off.

These sources comprise the "core" computational engine of Delphy. The web application that allows users to immediately and intuitively use Delphy (currently at [https://delphy.bio](https://delphy.bio)) is developed in collaboration with [Fathom Information Design](https://fathom.info), and its separately licensed sources are hosted [here](https://github.com/fathominfo/delphy-web).

**NOTE**: As of 17 Dec 2025, we have relicensed Delphy under an open-source [MIT license](LICENSE), and we have withdrawn our patent application, instead dedicating the relevant IP to the public domain.

References

• Preprint - [Delphy: scalable, near